+Open data
-Basic information
Entry | Database: PDB / ID: 7x4o | ||||||
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Title | Crystal structure of Vps17p PX from S. cerevisiae (Space) | ||||||
Components | Vacuolar protein sorting-associated protein 17Vacuole | ||||||
Keywords | LIPID BINDING PROTEIN / Phox domain Crystallized in International Space Station | ||||||
Function / homology | Function and homology information retromer, tubulation complex / retromer complex / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi / intracellular protein transport / endosome / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Maita, N. / Kohda, D. / Obita, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: Crystal structure of the PX domain of Vps17p from Saccharomyces cerevisiae. Authors: Obita, T. / Inaka, K. / Kohda, D. / Maita, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x4o.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x4o.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 7x4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/7x4o ftp://data.pdbj.org/pub/pdb/validation_reports/x4/7x4o | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16185.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: VPS17, PEP21, YOR132W, O3314, YOR3314W / Production host: Escherichia coli (E. coli) / References: UniProt: P32913 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 56.92 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 7.5 Details: 1.5M lithium sulfate, 0.1 M HEPES-Na, under a microgravity environment |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→44.85 Å / Num. obs: 22287 / % possible obs: 97.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 11.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.088 / Rrim(I) all: 0.124 / Χ2: 0.9 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.02→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1603 / CC1/2: 0.548 / Rpim(I) all: 0.561 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold2 Resolution: 2.02→44.85 Å / SU ML: 0.1986 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3147 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→44.85 Å
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Refine LS restraints |
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LS refinement shell |
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